PlanningAndMeetings

2013-10-01T16:16:35Z

Hilmar: Hilmar moved page PlanningAndMeetings to PhyloStars/Planning And Meetings

#REDIRECT [[PhyloStars/Planning And Meetings]]

PhyloStars/Planning And Meetings

2013-10-01T16:16:35Z

Hilmar: Hilmar moved page PlanningAndMeetings to PhyloStars/Planning And Meetings

HIP

2013-08-22T23:09:56Z

Hilmar: /* Leadership Team */

'''Hackathons, Interoperability, Phylogenies (HIP)''', a [http://www.nescent.org NESCent] working group, envision the future as a virtual phyloinformatics bazaar in which comparative data and phylogenies are saved, shared, annotated, liked, re-used, aggregated, mashed up, and linked in. In pursuit of this vision, the working group will stage a series of hackathons (intensive participant-driven code-development meetings) that empower early-career scientists to build the links of an emerging network of interoperable evolutionary resources [1].

* '''Hackathons''' - A hackathon is an event in which programmers ("hackers") meet to do collaborative programming. Hackathons naturally attract early-career researchers, and they provide a unique experience that combines learning, achievement and teamwork. Members of the HIP leadership team have extensive experience organizing and participating in hackathons (including 6 years of NESCent hackathons, as well as other bioinformatics hackathons).
* '''Interoperability''' - ISO defines "interoperability" as "The capability to communicate, execute programs, or transfer data among various functional units in a manner that requires the user to have little or no knowledge of the unique characteristics of those units" [http://jtc1sc36.org/doc/36N0646.pdf]. An operational definition is that interoperability exists when objectives can be achieved automatically, using human labor or "mind work" only where absolutely essential (e.g., for tasks that cannot or should not be automated, like fighting fires or answering the phone; see http://www.ariadne.ac.uk/issue24/interoperability/intro.html)
* '''Phylogenies''' - The focus of HIP is on supporting a variety of use-cases in evolutionary analysis that depend critically on making and using phylogenies (thus it is much broader than the problem of statistical inference of phylogenetic trees). This [http://informatics.nescent.org/wiki/UseCases list of use-cases] includes such problems as analyzing character evolution, building super-trees, making functional inferences about genes and proteins, and calibrating a molecular phylogeny with fossils.

== Hackathons ==

* '''[[PhyloStars]]: Developing a Socially Networked Bioinformatics Community-of-practice for the Evolution Research Community''' : To be announced soon
* '''[[Phylotastic | Phylotastic 2]]''' (Jan 28 to Feb 1, 2013) took place at iPlant headquarters in Tucson, Arizona, building on the success of the first phylotastic hackathon described below
* '''[[Phylotastic | Phylotastic: the Tree of Life, as you need it]]''' (June 4 to 8, NESCent) was HIP's first hackathon event. Woo hoo! At its January meeting, the HIP leadership team decided to throw away the playbook and opt for a new (for us) style of hackathon in which all participants are focused on a single over-arching goal. In this case, the goal is to '''build web-services infrastructures that provide the pruning, grafting, name-reconciliation, and translation operations needed for users to take advantage of the growing supply of megatrees.''' For more information:
** [[Phylotastic| project wiki ]]
** [[PhylotasticParticipants| participants page]]
** slide presentation in [http://bit.ly/xGvwRr ppt] or [http://bit.ly/wcQzMI PDF] format

== Partners ==

* [http://nescent.org NESCent]
* [http://synthesis.eol.org BioSynC]
* [http://www.iplantcollaborative.org iPlant]

== How to Get Involved ==

* HIP events will be advertised on the NESCent web site, the evoldir email list, and by other means
* if you have an idea for a hackathon target (something that a small team can do in a few days)
** discuss it with someone on the LT
** add it to the [[HIPTargetsAndIdeasList| targets & ideas list]]

== Links ==
* HIP [[HIPTargetsAndIdeasList| Targets & Ideas List]]
* Some thoughts on evolving a [[PhylotasticDataPolicy]]
* All pages on this wiki in [[:Category:HIP]]
* [[EvoIOWorkingGroupProposal | HIP working group proposal]]
* NESCent's [http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines guidelines] for proposing a hackathon
* [http://pipes.yahoo.com/pipes/pipe.run?_id=b269b02171b6411c4a27ae0714dc76da&_render=rss RSS feed of relevant projects]

== Leadership Team ==

HIP is managed by a leadership team (HIP-LT) consisting of the 3 PIs, 6 other members representing different dimensions of evolutionary informatics, and ad hoc members helping with planning of specific events. HIP-LT manages all aspects of the project-- advertising events, managing information resources, staging hackathons, and so on. The group meets electronically to conduct its business, and keeps a [[HIP_LT_Meetings|record of its meetings]].

{| border="1" cellspacing="0" cellpadding="5" align="left"
! Name
! width="25%" | Affiliation
! Image
!
! Name
! width="25%" | Affiliation
! Image
|-
| [http://www.ibbr.umd.edu/profiles/arlin-stoltzfus Arlin Stoltzfus]
| Fellow, IBBR (U Md) and Research Biologist, NIST
| [[Image:Arlin_head.jpg|Arlin Stoltzfus]]
|
| [[User:RutgerVos|Rutger Vos]]
| Marie Curie Research Fellow, University of Reading, UK
| [[Image:Rutger_Vos.jpg|Rutger Vos]]
|-
| [http://www.cs.nmsu.edu/~epontell Enrico Pontelli]
| Professor and Head, Department of Computer Science, New Mexico State University
| [[File:Enrico.jpg|100px|Enrico Pontelli]]
|
| [http://www.mendeley.com/profiles/karen-cranston/ Karen Cranston]
| National Evolutionary Synthesis Center (NESCent)
| [[File:Karen.jpg|100px|Karen Cranston]]
|-
| [http://www.matasci.info Naim Matasci]
| Scientific Lead, The iPlant Collaborative and Adjunct Assistant Professor, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| [[Image:Naim_matasci_face.jpg|100px|Naim Matasci]]
|
| [http://www.brianomeara.info Brian O'Meara]
| Assistant Professor, Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville
| [[Image:Brian_o%27meara_face.jpg|100px|Brian O'Meara]]
|-
| [http://www.rosenberglab.net/ Michael S Rosenberg]
| Associate Professor, School of Life Sciences & Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University
| [[File:MSRhead.jpg|100px|Michael S Rosenberg]]
|
| [http://people.oregonstate.edu/~sidlausb/ Brian Sidlauskas]
| Assistant Professor and Curator of Fishes, Oregon State University, Department of Fisheries and Wildlife
| [[Image:BrianHeadshot100.jpg]]
|-
| [http://www Mark Westneat]
| Curator and Chair of Zoology, Director, Biodiversity Synthesis Center, Field Museum of Natural History, Chicago
| [[Image:MarkStaffPhoto3.jpg|100px|Mark Westneat]]
|
| [[User:Hilmar|Hilmar Lapp]]
| National Evolutionary Synthesis Center (NESCent)
| [[File:Hilmar.jpg|100px|Hilmar Lapp]]
|}

Past members of the Leadership Team

{| border="1" cellspacing="0" cellpadding="5" align="left"
! Name
! width="25%" | Affiliation
! Image
!
! Name
! width="25%" | Affiliation
! Image
|-
| [http://www.datam0nk3y.org/hyphy/doku.php?id=sergei_l_kosakovsky_pond Sergei Kosakovsky Pond]
| Assistant Adjunct Professor, Department of Medicine, University of California, San Diego
| [[Image:Sergei.jpg|Sergei Kosakovsky Pond]]
|
| [http://www.medgen.ubc.ca/research/research_faculty/mwilkinson.htm Mark D Wilkinson]
| Associate Professor, Institute for Heart + Lung Health, University of British Columbia, Canada
| [[Image:Mark_Wilkinson.jpg|Mark Wilkinson]]
|}

[[Category:HIP]]

PhyloStars/BeforeAndAfter

2013-08-20T23:49:49Z

Hilmar: /* Assessment Goals */

== Assessment Goals ==

The things we would like to know, and how they ''might'' be measured. We would need to have a baseline for each one, based on current BioStars activity in all domains.

# Level of activity
#* number of new evolution-related questions (responses, answers) in the past month
#* up-votes and responses to existing evolution-related questions in the past month
# Responsiveness and effectiveness
#* how many questions get an answer within a week? a response?
#* what is the distribution of waiting times for answers? responses?
# Community
#* how many users respond to (view) evolution-related questions?
#* what is the average expertise of users in this community?
#* what is the apparent male:female ratio?
#* how many ''different'' people view evolution-related content in a month?

Caveat: the seasonality of academia-related efforts. Prior knowledge is that there are some really strange patterns, e.g., spike of activity just before winter break. If we do "before" in August, we really should wait until next August to do the "after".

== Methods and APIs ==

* You can get a picture of activity by clicking on the tag cloud. Activity can be sorted by votes. For example: http://www.biostars.org/show/tag/phylogenentics/?sort=votes&since=all%20time
* Everything can be measured retroactively, and there are API's to query site history. For example: a snapshot of the site 100 days ago can be obtained with http://www.biostars.org/api/stats/100/

==Before ==

=== relative topics ===
reported number of results based on August 20, 2013 search

phylostars
* phylostars 0

evolution
* evolution 760

molecular evolution
* ortholog* 1790
* paralog* 186

phylogenetics - interestingly, most references to "distance matrix" and "mega" are the phylogenetics meanings
* phylogen* 2920
* Phylip 241
* distance matrix 221
* MEGA 137
* MrBayes 124
* PAUP 70
* phylogram 36
* cladogram 4

population genetics
* population genetics 260
* coalescent 19
* McDonald-Kreitman 1

PhyloStars/BeforeAndAfter

2013-08-20T23:46:00Z

Hilmar: /* Assessment Goals */

== Assessment Goals ==

The things we would like to know, and how they ''might'' be measured. We would need to have a baseline for each one, based on current BioStars activity in all domains.

# Level of activity
#* number of new evolution-related questions (responses, answers) in the past month
#* up-votes and responses to existing evolution-related questions in the past month
# Responsiveness and effectiveness
#* how many questions get an answer within a week? a response?
#* what is the distribution of waiting times for answers? responses?
# Community
#* how many users respond to (view) evolution-related questions?
#* what is the average expertise of users in this community?
#* what is the apparent male:female ratio?
#* how many ''different'' people view evolution-related content in a month?

Caveat: the seasonality of academia-related efforts. Prior knowledge is that there are some really strange patterns, e.g., spike of activity just before winter break. If we do "before" in August, we really should wait until next August to do the "after".

==Before ==

=== relative topics ===
reported number of results based on August 20, 2013 search

phylostars
* phylostars 0

evolution
* evolution 760

molecular evolution
* ortholog* 1790
* paralog* 186

phylogenetics - interestingly, most references to "distance matrix" and "mega" are the phylogenetics meanings
* phylogen* 2920
* Phylip 241
* distance matrix 221
* MEGA 137
* MrBayes 124
* PAUP 70
* phylogram 36
* cladogram 4

population genetics
* population genetics 260
* coalescent 19
* McDonald-Kreitman 1

PhyloStars/BeforeAndAfter

2013-08-20T23:45:01Z

Hilmar:

AdvancingMIAPA

2013-02-03T00:32:46Z

Hilmar: Hilmar moved page AdvancingMIAPA to Advancing MIAPA

#REDIRECT [[Advancing MIAPA]]

Advancing MIAPA

2013-02-03T00:32:46Z

Hilmar: Hilmar moved page AdvancingMIAPA to Advancing MIAPA

== Factors shaping our conception of source-tree annotations ==

# what folks in the evoinfo community believe is the Minimal Information About a Phylogenetic Analysis (MIAPA)
#* The current synopsis of this is the MIAPA checklist from teh 2011 TDWG meeting.
# need to support assignment of credit (blame) for tree-producers and phylotastic service-providers
# need to support licensing that protects creators, resource-providers and end-users
# need to contribute to a credible provenance report for phylotastic-generated trees
#* e.g., a tree might be returned with information as follows (free text form): "This tree was obtained on Jan 29, 2013. An input list of 58 names was submitted to Taxosaurus, resulting in 45 valid species binomials ( list ). This list was sent to a pruner with instructions to prune out the indicated species from the phylogeny of Bininda-Emonds, et al. 2007. The resulting sub-tree with 40 species was scaled using teh DateLife service. "
# support the most common user criteria for phylotastic searching
#* limits on source trees
#** '''return tree with maximal coverage of list ::= { species }'''
#*** specify namespace of <list>
#** restrict by publication status (published or not)
#** restrict by publication year (e.g., no trees older than 5 years)
#** restrict by author (e.g., author = bininda-emonds)
#** restrict by other citation information (e.g., jrnl = index fungorum)
#** restrict by method
#*** '''use (exclude) trees made with method class = { parsimony, likelihood, Bayesian, distance, supertree, supermatrix, hand-crafted. . . } '''
#*** use (exclude) trees made with evolutionary model = { }
#*** '''use (exclude) trees made with software = { RaXML, BEAST, PAUP*, . . . }'''
#*** other restrictions (e.g., supertree, . . . )
#** restrict by availability of source data such as character matrix
#*** restrict by minimum number of characters in matrix
#** '''restrict by type of source data = { molecular, morphological, mixed } '''
#** restrict by annotation level = { platinum, gold, silver, bronze, polystyrene }
#** require feature
#*** '''require support values'''
#*** require rooting
#*** '''require branch lengths'''
#*** require fully resolved
#*** require other features
#* limits on phylotastic manipulations
#** disallow species substitution
#** disallow grafting of source trees
#** scaling: provide median age estimates
#** scaling: provide only lower age estimates
#** TNRS: prohibit fuzzy matching
#** TNRS: use matches from source = { NCBI, ITIS, et }
# support adequate annotation of the provenance of the resulting phylotastic tree
#* imagine that you have to publish an analysis using a phylogenetic tree-- how do you describe it? "The phylogeny of 40 mammal species was obtained via phylotastic (phylotastic.org
#* citation information

== Suggestions for MIAPA ontology ==
From annotation session on afternoon of 1/31.

* Add a class for parsimony under algorithm. [http://github.com/miapa/miapa/issues/7 Filed as Issue #7]

* It would be good to generate an instance of useMaximumLikelihood ("Maximum Likelihood algorithm") in MIAPA, so we don't have to create one for each annotation. [http://github.com/miapa/miapa/issues/8 Filed as Issue #8]

* Alternatively, maybe make classes of software (like PhyML or RAxML) implement ML algorithm, rather than having to assert it for each instance we create. Some software can use multiple algorithms, so we can't do this for each case.
** ''Note that in OWL classes cannot be asserted to have property values, only instances can. We can put property restrictions with existential quantification on classes, and a OWL reasoner could then infer that an instance must have at least one such property association (and thus a DL query should in principle return the instance), but this wouldn't work in an RDF triple store so that we could then actually query for these things in SPARQL.''
** ''Note also that there can be multiple swo:implements assertions for a software instance, so multiple algorithms can be easily asserted. However, this wouldn't the also say which of those implemented algorithms was the one utilized for the generation of the tree of alignment. The idea is that this would be evident from the miapa:'Parameter specification'.''

* Remove class for SILVA. [http://github.com/miapa/miapa/issues/9 Filed as Issue #9]

* Add new class for set of trees. [http://github.com/miapa/miapa/issues/10 Filed as Issue #10]

== Lessons learned from tree-finding and annotation ==

* data frequently is not readily accessible online
** e.g. Jetz one must go to birdtree.org
** e.g., we obtained hymenoptera tree by pers. communication from Peters
** only one of the studies has trees in TreeBASE (GEBA)
** another study has a tree in Dryad (Smith)
* authors often don't provide minimal information explicitly
** whether or not a tree is rooted is usually not explicit
*** e.g., taxonomic hierarchies (APG, ToLWeb, NCBI) imply rootedness
*** e.g., Peters, et al 2011 never invokes the term "root" but we infer rooting from the description of outgroups not present in the final tree
** the methodology is largely unexplained for curated or hand-crafted taxonomic frameworks like APGIII or NCBI
* a study frequently has several trees by slightly different methods, but the checklist seems to imply one method
** e.g., Goloboff molecules only vs. molecules with morphology
** e.g., Bininda-Emonds best dates vs min dates vs max dates
* sometimes a study has many trees that all represent outputs of the same method
** e.g., Jetz provide a large sample from the posterior distribution
* process of constructing tree does not follow sequences--> alignment--> tree
** e.g., supertree method in Bininda-Emonds
** e.g., hand-crafted APG, Smith, trees
* process of constructing tree cannot be condensed easily
** e.g., Goloboff, iterative procedure with divide-and-conquer search to find parsimony tree ("tree fuse" & "sector" search repeated)
** GEBA tree, { missing explanation }
** partitioned alignment (e.g., Smith, et al), but miapa implies "model of evolution" as though there were only one, whereas in Peters, et al there are 2 models for 2 partitions
* clustering to define orthologs not included in checklist, but seems important
** Smith phlawd, alignment: no pre-orthology.
* mixed data is common
** Goloboff has morpho and molecular
** multiple studies have DNA (e.g., SSU rDNA) and protein sequences
* concatenated alignments are common, e.g., multiple proteins
** this means accession:OTU mapping is not 1:1 but many to one
* not encountered in our inputs but sometimes the OTU is <genus_sp> and the data are fused from multiple species (this is common in MorphoBank)
* many important trees do not have branch lengths
** e.g., APGIII is a taxonomic framework
** e.g., some supertrees don't have branch lengths
* do binomials count as meaningful external identifiers for OTUs?
** in some cases, the methods make clear that these come from a specific source
*** e.g., Goloboff names clearly come directly from NCBI via their bioinfo pipeline
*** e.g., Bininda-Emonds publication declares that naming authority is Wilson & Roeder (Mammal Species of the World)
*** e.g., NCBI taxonomy comes as a database dump wth taxids and synonyms, so it represents its own authority
** usually the naming authority is not clear
* was any study straightforward?
* OTUs checklist question may be redundant: why have external identifier and then ask for collections information?
* OTU external refs in checklist: not applicable for supertree methods, consensus methods, hand-crafted

== MIAPA Resources ==
* The main [[MIAPA]] page. Primarily:
** [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist MIAPA draft checklist] from TDWG 2011 workshop.
** Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
** [http://www.slideshare.net/ElliottHauser/phylogenetics-data-provenance-survey-results Slideshow] with some results from the [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey MIAPA community survey] orchestrated by the Open Tree of Life project in fall 2012.
* Development:
** [http://github.com/miapa/miapa MIAPA repo on Github]
* Ontologies
** [http://www.evolutionaryontology.org/cdao CDAO]
** [http://www.w3.org/TR/prov-o/ W3C Provenance Ontology]
** [http://code.google.com/p/information-artifact-ontology/ Information Artefact Ontology]
** [http://theswo.sourceforge.net/ Software Ontology] (includes the [http://edamontology.org/ EDAM ontologies])
** [http://bioportal.bioontology.org/ontologies/49276?p=terms phylont] from [http://arnetminer.org/publication/phylont-a-domain-specific-ontology-for-phylogeny-analysis-3601839.html;jsessionid=E93A88FA38E826E1113A957BBA5BB352.tt Maryam Panahiazar, et al]. (We did not use this.)

== Annotation ==
* representation of metadata: [http://www.nexml.org NeXML]
* some stuff that Rutger did mapping the metadata from ToLWeb XML format onto semantic annotations in NeXML.
** ToLWeb XML described here: http://tolweb.org/tree/home.pages/downloadtree.html
** a simple script that does the conversion: https://github.com/ncbnaturalis/bio-phylo/blob/master/experimental/tolconvert.pl
** Here's an example input file: https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol.xml
** Here's the resulting output file (indented): https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol-nexml-pp.xml

2013-01-31T23:03:34Z

Hilmar: /* MIAPA */

=== Factors shaping our conception of source-tree annotations ===

# what folks in the evoinfo community believe is the Minimal Information About a Phylogenetic Analysis (MIAPA)
#* The current synopsis of this is the MIAPA checklist from teh 2011 TDWG meeting.
# need to support assignment of credit (blame) for tree-producers and phylotastic service-providers
# need to support licensing that protects creators, resource-providers and end-users
# need to contribute to a credible provenance report for phylotastic-generated trees
#* e.g., a tree might be returned with information as follows (free text form): "This tree was obtained on Jan 29, 2013. An input list of 58 names was submitted to Taxosaurus, resulting in 45 valid species binomials ( list ). This list was sent to a pruner with instructions to prune out the indicated species from the phylogeny of Bininda-Emonds, et al. 2007. The resulting sub-tree with 40 species was scaled using teh DateLife service. "
# support the most common user criteria for phylotastic searching
#* limits on source trees
#** '''return tree with maximal coverage of list ::= { species }'''
#*** specify namespace of <list>
#** restrict by publication status (published or not)
#** restrict by publication year (e.g., no trees older than 5 years)
#** restrict by author (e.g., author = bininda-emonds)
#** restrict by other citation information (e.g., jrnl = index fungorum)
#** restrict by method
#*** '''use (exclude) trees made with method class = { parsimony, likelihood, Bayesian, distance, supertree, supermatrix, hand-crafted. . . } '''
#*** use (exclude) trees made with evolutionary model = { }
#*** '''use (exclude) trees made with software = { RaXML, BEAST, PAUP*, . . . }'''
#*** other restrictions (e.g., supertree, . . . )
#** restrict by availability of source data such as character matrix
#*** restrict by minimum number of characters in matrix
#** '''restrict by type of source data = { molecular, morphological, mixed } '''
#** restrict by annotation level = { platinum, gold, silver, bronze, polystyrene }
#** require feature
#*** '''require support values'''
#*** require rooting
#*** '''require branch lengths'''
#*** require fully resolved
#*** require other features
#* limits on phylotastic manipulations
#** disallow species substitution
#** disallow grafting of source trees
#** scaling: provide median age estimates
#** scaling: provide only lower age estimates
#** TNRS: prohibit fuzzy matching
#** TNRS: use matches from source = { NCBI, ITIS, et }
# support adequate annotation of the provenance of the resulting phylotastic tree
#* imagine that you have to publish an analysis using a phylogenetic tree-- how do you describe it? "The phylogeny of 40 mammal species was obtained via phylotastic (phylotastic.org
#* citation information

=== Lessons learned from tree-finding and annotation ===

* data frequently is not readily accessible online
** e.g. Jetz one must go to birdtree.org
** e.g., we obtained hymenoptera tree by pers. communication from Peters
** only one of the studies has trees in TreeBASE (GEBA)
** another study has a tree in Dryad (Smith)
* authors often don't provide minimal information explicitly
** whether or not a tree is rooted is usually not explicit
*** e.g., taxonomic hierarchies (APG, ToLWeb, NCBI) imply rootedness
*** e.g., Peters, et al 2011 never invokes the term "root" but we infer rooting from the description of outgroups not present in the final tree
** the methodology is largely unexplained for curated or hand-crafted taxonomic frameworks like APGIII or NCBI
* a study frequently has several trees by slightly different methods, but the checklist seems to imply one method
** e.g., Goloboff molecules only vs. molecules with morphology
** e.g., Bininda-Emonds best dates vs min dates vs max dates
* sometimes a study has many trees that all represent outputs of the same method
** e.g., Jetz provide a large sample from the posterior distribution
* process of constructing tree does not follow sequences--> alignment--> tree
** e.g., supertree method in Bininda-Emonds
** e.g., hand-crafted APG, Smith, trees
* process of constructing tree cannot be condensed easily
** e.g., Goloboff, iterative procedure with divide-and-conquer search to find parsimony tree ("tree fuse" & "sector" search repeated)
** GEBA tree, { missing explanation }
** partitioned alignment (e.g., Smith, et al), but miapa implies "model of evolution" as though there were only one, whereas in Peters, et al there are 2 models for 2 partitions
* clustering to define orthologs not included in checklist, but seems important
** Smith phlawd, alignment: no pre-orthology.
* mixed data is common
** Goloboff has morpho and molecular
** multiple studies have DNA (e.g., SSU rDNA) and protein sequences
* concatenated alignments are common, e.g., multiple proteins
** this means accession:OTU mapping is not 1:1 but many to one
* not encountered in our inputs but sometimes the OTU is <genus_sp> and the data are fused from multiple species (this is common in MorphoBank)
* many important trees do not have branch lengths
** e.g., APGIII is a taxonomic framework
** e.g., some supertrees don't have branch lengths
* do binomials count as meaningful external identifiers for OTUs?
** in some cases, the methods make clear that these come from a specific source
*** e.g., Goloboff names clearly come directly from NCBI via their bioinfo pipeline
*** e.g., Bininda-Emonds publication declares that naming authority is Wilson & Roeder (Mammal Species of the World)
*** e.g., NCBI taxonomy comes as a database dump wth taxids and synonyms, so it represents its own authority
** usually the naming authority is not clear
* was any study straightforward?
* OTUs checklist question may be redundant: why have external identifier and then ask for collections information?
* OTU external refs in checklist: not applicable for supertree methods, consensus methods, hand-crafted

== MIAPA Resources ==
* The main [[MIAPA]] page. Primarily:
** [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist MIAPA draft checklist] from TDWG 2011 workshop.
** Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
** [http://www.slideshare.net/ElliottHauser/phylogenetics-data-provenance-survey-results Slideshow] with some results from the [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey MIAPA community survey] orchestrated by the Open Tree of Life project in fall 2012.
* Ontologies
** [http://bioportal.bioontology.org/ontologies/49276?p=terms phylont] from [http://arnetminer.org/publication/phylont-a-domain-specific-ontology-for-phylogeny-analysis-3601839.html;jsessionid=E93A88FA38E826E1113A957BBA5BB352.tt Maryam Panahiazar, et al]
** [http://www.evolutionaryontology.org/cdao CDAO]
* Development:
** [http://github.com/miapa/miapa MIAPA repo on Github]
** Template development after the [https://github.com/phylotastic/treestore/tree/master/terms TNRS ontology] developed at (and after) Phylotastic I.

== Annotation ==
* representation of metadata: [http://www.nexml.org NeXML]
* some stuff that Rutger did mapping the metadata from ToLWeb XML format onto semantic annotations in NeXML.
** ToLWeb XML described here: http://tolweb.org/tree/home.pages/downloadtree.html
** a simple script that does the conversion: https://github.com/ncbnaturalis/bio-phylo/blob/master/experimental/tolconvert.pl
** Here's an example input file: https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol.xml
** Here's the resulting output file (indented): https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol-nexml-pp.xml